Dans ce rapport il y a les visualisations graphiques des analyses RNAseq de l’effet de Shavenbaby dans les cellules S2.
library(Glimma)
load("~/Documents/RNAseq/RNAseq_S2/RNaseq_environnement.RData")glimmaMA(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = diffGeneActContr, anno = annoAct , groups = groups, display.columns = c("ID","DE_Act","logFC_ActvsCtrl","BH_ActvsCtrl"),status.cols = c("red","grey","green"), main = "ActvsCtrl", html = "ActVsCtrl/GLimmaMAplot_ActvsCtrl.html")## Saving widget...## ActVsCtrl/GLimmaMAplot_ActvsCtrl.html generated.glimmaVolcano(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = diffGeneActContr, anno = annoAct , groups = groups, display.columns = c("DE_Act","logFC_ActvsCtrl","BH_ActvsCtrl"),status.cols = c("red","grey","green"), main = "ActvsCtrl", html = "ActVsCtrl/GLimmaVolcanoplot_ActvsCtrl.html")## Saving widget...## ActVsCtrl/GLimmaVolcanoplot_ActvsCtrl.html generated.glimmaVolcano(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = diffGeneActContr, anno = annoAct , groups = groups, display.columns = c("DE_Act","logFC_ActvsCtrl","BH_ActvsCtrl"),status.cols = c("red","grey","green"), main = "ActvsCtrl")glimmaVolcano(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"), status.cols = c("grey","grey","purple"), main = "ActvsCtrl", html = "ActvsCtrl/GLimmaVolcanoplot_ActvsCtrl_directtarget.html")## Saving widget...## ActvsCtrl/GLimmaVolcanoplot_ActvsCtrl_directtarget.html generated.glimmaVolcano(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"), status.cols = c("grey","grey","purple"), main = "ActvsCtrl")glimmaMA(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "ActvsCtrl", html = "ActvsCtrl/GLimmaMAplot_ActvsCtrl_direct.html")## Saving widget...## ActvsCtrl/GLimmaMAplot_ActvsCtrl_direct.html generated.glimmaMA(lrt.2$ActVsContr, dge = lrt.2$ActVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "ActvsCtrl")glimmaMA(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = diffGeneRepvsCs, anno = annoRep , groups = groups, display.columns = c("ID","DE_Rep","logFC_RepvsCtrl","BH_RepvsCtrl"),status.cols = c("red","grey","green"), main = "RepvsCtrl", html = "RepvsCtrl/GLimmaMAplot_RepvsCtrl.html")## Saving widget...## RepvsCtrl/GLimmaMAplot_RepvsCtrl.html generated.glimmaMA(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = diffGeneRepvsCs, anno = annoRep , groups = groups, display.columns = c("ID","DE_Rep","logFC_RepvsCtrl","BH_RepvsCtrl"),status.cols = c("red","grey","green"), main = "RepvsCtrl")glimmaVolcano(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = diffGeneRepvsCs, anno = annoRep , groups = groups, display.columns = c("ID","DE_Rep","logFC_RepvsCtrl","BH_RepvsCtrl"),status.cols = c("red","grey","green"), main = "RepvsCtrl", html = "RepvsCtrl/GLimmaVolcanoplot_RepvsCtrl.html")## Saving widget...## RepvsCtrl/GLimmaVolcanoplot_RepvsCtrl.html generated.glimmaVolcano(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = diffGeneRepvsCs, anno = annoRep , groups = groups, display.columns = c("ID","DE_Rep","logFC_RepvsCtrl","BH_RepvsCtrl"), status.cols = c("red","grey","green"), main = "RepvsCtrl")glimmaVolcano(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "RepvsCtrl", html = "RepvsCtrl/GLimmaVolcanoplot_RepvsCtrl_directtarget.html")## Saving widget...## RepvsCtrl/GLimmaVolcanoplot_RepvsCtrl_directtarget.html generated.glimmaVolcano(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "RepvsCtrl")glimmaMA(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "RepvsCtrl", html = "RepvsCtrl/GLimmaMAplot_RepvsCtrl_direct.html")## Saving widget...## RepvsCtrl/GLimmaMAplot_RepvsCtrl_direct.html generated.glimmaMA(lrt.2$RepVsContr, dge = lrt.2$RepVsContr,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "RepvsCtrl")glimmaMA(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = diffGeneActRep, anno = annoActRep , groups = groups, display.columns = c("ID","DE_ActRep","logFC_ActvsRep","BH_ActvsRep"),status.cols = c("red","grey","green"), main = "ActvsRep", html = "ActvsRep/GLimmaMAplot_ActvsRep.html")## Saving widget...## ActvsRep/GLimmaMAplot_ActvsRep.html generated.glimmaMA(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = diffGeneActRep, anno = annoActRep ,groups = groups, display.columns = c("ID","DE_ActRep","logFC_ActvsRep","BH_ActvsRep"),status.cols = c("red","grey","green"), main = "ActvsRep")glimmaVolcano(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = diffGeneActRep, anno = annoActRep , groups = groups, display.columns = c("ID","DE_ActRep","logFC_ActvsRep","BH_ActvsRep"),status.cols = c("red","grey","green"), main = "ActvsRep", html = "ActvsRep/GLimmaVolcanoplot_ActvsRep.html")## Saving widget...## ActvsRep/GLimmaVolcanoplot_ActvsRep.html generated.glimmaVolcano(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = diffGeneActRep, anno = annoActRep , groups = groups, display.columns = c("ID","DE_ActRep","logFC_ActvsRep","BH_ActvsRep"), status.cols = c("red","grey","green"), main = "ActvsRep")glimmaVolcano(lrt.2$ActVsRep, dge = lrt.2$ActVsRep ,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "ActvsRep", html = "ActvsRep/GLimmaVolcanoplot_ActvsRep_directtarget.html")## Saving widget...## ActvsRep/GLimmaVolcanoplot_ActvsRep_directtarget.html generated.glimmaVolcano(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "ActvsRep")glimmaMA(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "ActvsRep", html = "ActvsRep/GLimmaMAplot_ActvsRep_direct.html")## Saving widget...## ActvsRep/GLimmaMAplot_ActvsRep_direct.html generated.glimmaMA(lrt.2$ActVsRep, dge = lrt.2$ActVsRep,counts= RNAseq_norm$counts , status = anno_direct_target$directgene, anno = anno_direct_target , groups = groups, display.columns = c("directgene","direct", "DE_Act", "DE_Rep","DE_ActRep", "logFC_ActCtrl","logFC_RepCtrl","logFC_ActRep"),status.cols = c("grey","grey","purple"), main = "ActvsRep")